Research workbench
Thrombin in complex with inhibitor
Analyse Thrombin in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BAM
- Type
- protein
- Length
- 286 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-1
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- MM9, NAG, NA
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 15% helix, 35% strand | P00734 |
| D | Hirudin variant-1 | protein | 10 | 30% helix, 0% strand | P01050 |
Ligands and binding sites
- MM9 · (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(dimethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- NA · Sodium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.54 | 0.77 | 39 | MM9 |
| 2 | 78 | 0.38 | 0.77 | 20 | empty |
| 3 | 50 | 0.26 | 0.74 | 11 | empty |
| 4 | 52 | 0.25 | 0.72 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1109 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 654 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00734
- Every structure of UniProt P01050
- Elsewhere: RCSB PDB 4BAM · PDBe 4BAM · UniProt P00734 · UniProt P01050
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